Willian had already undergone a medical ahead of a potential move to White Hart Lane when the Blues made their offer to Anzhi Makhachkala.
The Brazil midfielder, who is expected to cost whichever club he ends up at a fee of around £30m, started to create doubts over a move to Spurs when he revealed he was 'considering his options' after the medical.
Willian had been seen as something of a priority signing for Tottenham, who are still expected to see Gareth Bale leave before the end of the transfer window.
He was targeted by Spurs boss Andre Villas-Boas when at Chelsea and had also been linked with Liverpool.
When asked if Willian was about to join, Mourinho nodded and then said: "I think he's already made his decision.
"I don't like to speak before time because football can be crazy. I know what the player wants, so in this moment we cannot hide. That is a possibility.
"You have to do the medical before, but the best thing to do is to do the medical in secret. If the player is fine, you can sign him. If the player is not fine you don't destroy his career.
"Every one of us managers will say we are happy with our squad, but we are always unhappy. We always want something more, something of more quality and never close the door to the possibility of adding more quality.
"Before Aston Villa I told you we have Plan B and Plan C so I was letting the door open to other possibilities.
"I want a 22 player squad so if somebody comes, somebody leaves. Do we need to sell, no we don't. Do we need to loan, probably yes because I don't like to work with big squads. I like to work with a small group of players, and I say 22 is a perfect number for our needs in different competitions."
Mourinho was asked if speculation about Juan Mata's possible departure from Stamford Bridge was accurate, and he added: "No speculation. He is a player we all like, a player we all want to keep. We want more quality in the team, not less."
Speaking on Thursday night after Spurs had beaten Dinamo Tbilisi in the Europa League play-off tie, Villas-Boas conceded he knew nothing of his old club's interest in Willian.
Villas-Boas said: "We were just involved in a game so unfortunately I can't give you further information.
"I confirmed our interest in the player. Everything is possible, but I'm not aware of the circumstances because of our involvement in the (Dinamo) game.
"I don't want it to be a distraction over what we achieved here tonight."